Modelling
3rd field of activity
Modelling the effects of sparsely and densely ionising radiation
Modelling the biological effects of radiation is of interest for a general understanding of radiation action as well as for applications in radiation therapy and radiation protection. As a consequence of the complexity of the biological processes, however, it cannot be expected that a single model will be able to represent all relevant aspects. Therefore different approaches will be appropriate for different specific aims/goals.
For example, an increase of the efficiency of ion beam radio therapy can be expected when using inhibitors of proteins playing a key role in the cellular radiation response. Modelling the binding of these inhibitors and the resulting prediction of the affinity can play an important role for the optimization of synthetic inhibitors. This finally can lead to a transfer from basic research to pharmacological use.
Due to the large number of proteins involved in the processing of radiation damage, a systems biology oriented, network based approach is required here. Radiation type and thus the quality of radiation damage will have a major impact on the processing of damages. A network based analysis of experimental data will thus also help to decipher the different paths of the repair network.
For a quantitative prediction of biological damage on the cellular and tissue level empirical models play an important role. For applications in ion beam therapy, these models are for example used to determine the increased effectiveness of densely ionizing radiation in normal and tumor tissues. Modelling the increased yield of initial damages and their dependence on the oxygen supply represent the key aspects which will be investigated.
The planned work comprises modelling on different length and time scales. On the molecular level, the binding of proteins will be modelled. On the cellular level, the work will focus on the interaction and regulation of proteins and protein networks. Furthermore, the impact of the yield and microscopic distribution of initial damages on the effectiveness of different radiation types for cell killing, cell transformation and induction of secondary tumors will be investigated.
Prof. Dr. Barbara Drossel (TU Darmstadt, Physics)
Background: After a damage induced by ionizing radiation, proteins for repair and signalling are recruited to the damaged region and form within a few minutes foci that extend over millions of base pairs of the adjacent DNA. Hereby, the different processes mutually depend on each other. For double strand breaks (DSBs), these processes are the recruitment of the MRN complex, of MDC1 and additional proteins, the phosphorylation of the histone H2AX and the activation of ATM (1-4). Spatially and temporally resolved measurement of the recruitment of, e.g., NBS1 shows that after irradiation with a low LET the formation of the focus takes about 10 minutes, while it takes only 3 minutes after irradation with a higher LET. This latter duration does not decrease further with a further increased LET.
Goal of the project: We will develop models that reproduce the dependence on the LET and other signatures of the recruitment kinetics. These models shall include rate equations for the binding and the dissociation of the mentioned proteins or for their phosphorylation. They shall also include stochastic and spatial effects. These theoretical investigations shall be performed in close collaboration with the experimental groups of the Graduiertenkolleg (Projects 1E Jakob, 1A Löbrich, 1B Cardoso und 1C Rapp). Since the networks involved in the different repair pathways are mutually connected, we will also model other repair pathways.
Schedule: First, we will establish a model for the formation of a focus around a single DSB. This model shall be compared with what is known from the literature and from experiments performed in Darmstadt. Then, the model shall be extended to larger LET, and it shall include possible mechanisms for the limitation of the growth speed of foci. The insights gained from project 3B (Scholz) concerning the relation between the number of DSBs and the number of foci, as well as the results of projects 1C (Rapp) and 1B (Cardoso) concerning the changes in the structure of chromatin shall be taken into account. The model will implement the facts that the recruitment process at the break is different from that along the adjacent DNA, and that the activity and concentration of ATM depends on space and time. Since recruitment dynamics depend on the affinities of the molecules, the project has also a link to project 3C (Hamacher).
In parallel, our group will work on compiling information about the wider network that is involved in the decision making about the cell fate after radiation damage. These decisions involve cell cycle arrest, repair, and apoptosis. The results of this part shall be connected to those experimental projects that deal with this type of decision (Projects 2A Thiel, 1A Löbrich, 2F Rödel, 2B Fournier, 2C Dencher).
Literatur:
(1) Ma et al. (2005) Proc Natl Acad Sci USA; 102:14266-71.
(2) Qi et al. (2007) Biosystems; 90:698-706.
(3) Politi et al. (2005) Mol Cell; 19:679-90.
(4) Dinant et al. (2009) J Cell Biol; 185:21-6
PD Dr. Michael Scholz (GSI Biophysics)
Background: The Local Effect Model (LEM) is based on detailed modelling of the initial double strand break (DSB) distribution induced by ion traversals through the cell nucleus. According to the model, the increased effectiveness of ions can be traced back partially to the increased yield of DSBs, resulting from the proximity of two single strand breaks (1,2). The γH2AX-assay allows to experimentally determine the DSB yield. The standard method is based on counting the number of γH2AX foci, and it could be shown that using the appropriate analysis conditions a clear correlation between foci number and DSB is observed. However, if multiple DSBs are induced close together, in general this cannot be resolved with the foci counting method. Flowcytometry represents an alternative method in this case, because it is based on determining the integral fluorescence signal, which is expected to be proportional to the number of DSB without being affected by the proximity of DSB. By comparing the foci counting and flow cytometric method the number of multiple DSB within individual foci can be assessed.
Aim of the project: To test predictions of the LEM concerning the increased yield of DSBs for ion beam irradiation by comparison to experimental data based on the γH2AX flow cytometry assa (3).
Work plan: Different cell lines (e.g. CHO cells) will be irradiated with ion beams and the DSB induction will be quantified using the γH2AX flow cytometry assay. The experiments will focus on a detailed systematic investigation over a broad range of different ion species and beam energies. These will allow to analyse a correspondingly broad range of ionization densities, expected to lead to a significant variation of DSB induction yields. In particular, comparing different ions at the same LET value will allow to study the impact of track structure. Measured DSB yields will be compared with values predicted by the LEM and will help to improve the accurate description of the local dose distribution within the particle track.
Furthermore, the accurate prediction of the yield will also affect the modelling of the spatial distributions of DSB within the nucleus and in particular the proximity of DSBs. This is expected to significantly affect the reparability of lesions and the project is thus closely related to project 1A. Furthermore, the project is also connected to project 1E, since proximity of DSB will have an impact on the repair processes depending on the dynamic properties of the chromatin structure. In addition, the yield and spatial distribution of DSB are assumed to be relevant for the recruitment of repair proteins, building thus a bridge to project 3A.
References:
(1) Elsässer und Scholz (2007) Radiat Res; 167:319-29.
(2) Elsässer et al. (2008) Int J Radiat Oncol Biol Phys; 71:866-72.
(3) MacPhail et al. (2003) Radiat Res; 159:759-67.
Prof. Dr. Kay Hamacher (Bioinformatics& Theo. Biology)
Background: The efficiency of radiation therapy is reduced by damage responses within tumor cells. Up to now, there are no theoretically sound, multi-scale studies on design of functional ligands to inhibit this damage response.
We focus on two systems: a) the protein degradation of the proteasome and b) the DNA-protein repair complex of DNA, Ku-homodimer and PKCS involved in the Non-homologous End-joining (NHEJ) process.
Furthermore, the evolution of the DNA-repair mechanism is not fully understood at the single molecule level. In the long run this issue will be addressed in the project, too.
Goal of the project: a) identification of radio-sensitizing lead structures to support other efforts in this graduate school (project 2E Schmidt); b) understanding the basis of the NHEJ modulation by low-mass compounds; and c) to quantify the evolvability of the damage response at the single molecule level and annotate this biophysically.
Work plan: a) molecular topologies of a known proteasom inhibitors need to be created. These will be docked by established algorithms and more modern optimization-algorithms to understand the competitive binding on the proteolytic site of the β5-subunit of the 20S-proteasome (1,2). Ligand flexibility and covalent binding of proteasome inhibitor at Thr-rests in the proteasome require a multi-scale approach. b) Using coarse-grained molecular dynamics, new inhibitory mechanisms on the repair of double-stranded breaks and the conformational transitions in the DNA-Ku-PKcs-Komplex will be untertaken (3).
References:
(1) Hamacher (2007) J Comp Phys; 227:1500-9.
(2) Hamacher (2007) J Comp Chem; 28:2576-80.
(3) Hamacher und McCammon (2006) J Chem Theo Comp; 2:873.